--- OA_place: repository OA_type: free access _id: '18648' abstract: - lang: eng text: "Statistical causal learning in genomics relies on the instrumental variable method of\r\nMendelian Randomization (MR). Currently, an overwhelming number of MR studies\r\npurport to show causal relationships among a wide range of risk factors and outcomes.\r\nHere, we show that selecting instrument variables from genome-wide association study\r\nestimates leads to high false discovery rates for many MR approaches, which can be\r\ngreatly reduced by employing a graphical inference approach which: (i) explicitly tests\r\ninstrumental variable assumptions; (ii) distinguishes direct from indirect factors in very\r\nhigh-dimensional data; (iii) discriminates pleiotropic from trait-specific markers, controlling for LD genome-wide; (iv) accommodates rare variants and binary outcomes in a\r\nprincipled way; and (v) identifies potential unobserved latent confounding. For 17 traits\r\nand 8.4M variants recorded for 458,747 individuals in the UK Biobank, we show that\r\nstandard MR analysis gives an abundance of findings that disappear under stringent\r\nassumption checks, with many relationships reflecting potential unmeasured confounding. This implies that mixtures of temporal precedence and potential for reverse-causality\r\nprohibit understanding the underlying nature of phenotypic and genetic correlations in\r\nbiobank data. We propose that well-curated longitudinal records are likely needed and\r\nthat our approach provides a first-step toward robust principled screening for potential\r\ncausal links.\r\n" acknowledged_ssus: - _id: ScienComp acknowledgement: "We thank Zoltan Kutalik and members of the Robinson group \r\nat ISTA for their comments, which improved this manuscript. This work was funded \r\nby a research collaboration agreement between Boehringer Ingelheim and the research \r\ngroup of MRR at the Institute of Science and Technology Austria. Additional funding \r\nwas also provided by an SNSF Eccellenza Grant to MRR (PCEGP3-181181), and by \r\ncore funding from the Institute of Science and Technology Austria. We would like \r\nto acknowledge the participants and investigators of the UK Biobank study. High- \r\nperformance computing was supported by the Scientific Service Units (SSU) of IST \r\nAustria through resources provided by Scientific Computing (SciComp). " article_processing_charge: No author: - first_name: Nick N full_name: Machnik, Nick N id: 3591A0AA-F248-11E8-B48F-1D18A9856A87 last_name: Machnik orcid: 0000-0001-6617-9742 - first_name: Seyed Mahdi full_name: Mahmoudi, Seyed Mahdi id: b9f6d5ef-7774-11eb-a47f-df2c75c02ee7 last_name: Mahmoudi - first_name: Malgorzata full_name: Borczyk, Malgorzata last_name: Borczyk - first_name: Ilse full_name: Krätschmer, Ilse id: 30d4014e-7753-11eb-b44b-db6d61112e73 last_name: Krätschmer orcid: 0000-0002-5636-9259 - first_name: Markus J. full_name: Bauer, Markus J. last_name: Bauer - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 citation: ama: Machnik NN, Mahmoudi SM, Borczyk M, Krätschmer I, Bauer MJ, Robinson MR. Causal inference for multiple risk factors and diseases from genomics data. bioRxiv. 2024. doi:10.1101/2023.12.06.570392 apa: Machnik, N. N., Mahmoudi, S. M., Borczyk, M., Krätschmer, I., Bauer, M. J., & Robinson, M. R. (2024). Causal inference for multiple risk factors and diseases from genomics data. bioRxiv. https://doi.org/10.1101/2023.12.06.570392 chicago: Machnik, Nick N, Seyed Mahdi Mahmoudi, Malgorzata Borczyk, Ilse Krätschmer, Markus J. Bauer, and Matthew Richard Robinson. “Causal Inference for Multiple Risk Factors and Diseases from Genomics Data.” BioRxiv, 2024. https://doi.org/10.1101/2023.12.06.570392. ieee: N. N. Machnik, S. M. Mahmoudi, M. Borczyk, I. Krätschmer, M. J. Bauer, and M. R. Robinson, “Causal inference for multiple risk factors and diseases from genomics data,” bioRxiv. 2024. ista: Machnik NN, Mahmoudi SM, Borczyk M, Krätschmer I, Bauer MJ, Robinson MR. 2024. Causal inference for multiple risk factors and diseases from genomics data. bioRxiv, 10.1101/2023.12.06.570392. mla: Machnik, Nick N., et al. “Causal Inference for Multiple Risk Factors and Diseases from Genomics Data.” BioRxiv, 2024, doi:10.1101/2023.12.06.570392. short: N.N. Machnik, S.M. Mahmoudi, M. Borczyk, I. Krätschmer, M.J. Bauer, M.R. Robinson, BioRxiv (2024). corr_author: '1' date_created: 2024-12-11T10:42:59Z date_published: 2024-08-10T00:00:00Z date_updated: 2026-07-16T22:30:22Z day: '10' department: - _id: MaRo doi: 10.1101/2023.12.06.570392 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2023.12.06.570392 month: '08' oa: 1 oa_version: Preprint project: - _id: 9B8D11D6-BA93-11EA-9121-9846C619BF3A grant_number: PCEGP3_181181 name: Improving estimation and prediction of common complex disease risk - _id: bd936e6f-d553-11ed-ba76-a82299f63e8c grant_number: '590359' name: Advanced statistical modelling to facilitate more accurate characterisation of disease phenotypes, improved genetic mapping, and effective therapeutic hypothesis generation publication: bioRxiv publication_status: published related_material: record: - id: '18642' relation: dissertation_contains status: public status: public title: Causal inference for multiple risk factors and diseases from genomics data tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2024' ... --- OA_place: publisher _id: '18661' abstract: - lang: eng text: "Across the tree of life, distinct designs of cellular membranes have evolved that are both stable\r\nand flexible. In bacteria and eukaryotes this trade-off is accomplished by single-headed lipids\r\nthat self-assemble into flexible bilayer membranes. By contrast, archaea in many cases possess\r\nboth bilayer and double-headed, monolayer spanning bolalipids. This composition is believed\r\nto enable extremophile archaea to survive harsh environments. Here, through the creation of a\r\nminimal computational model for bolalipid membranes, we discover trade-offs when forming\r\nmembranes using lipids of a single type. Similar to living archaea, we can tune the stiffness of\r\nbolalipid molecules. We find that membranes made out of flexible bolalipid molecules resemble\r\nbilayer membranes as they can adopt U-shaped conformations to enable higher curvatures.\r\nConversely, rigid bolalipid molecules, like those found in archaea at higher temperatures,\r\npreferentially take on a straight conformation to self-assemble into liquid membranes that are\r\nstable, stiff, prone to pore formation, and which tear during membrane reshaping. Strikingly,\r\nhowever, our analysis reveals that it is possible to achieve the best of both worlds – membranes\r\nthat are fluid, stable at high temperatures and flexible enough to be reshaped without leaking –\r\nthrough the inclusion of a small fraction of bilayer lipids into a bolalipid membrane. Additionally,\r\nthe curvature-dependent softening of bolalipid membranes made of lipids with tension-sensitive\r\nconformation can also enable high rigidity at low curvatures while softening at high curvatures,\r\nmaking the membrane effectively a plastic material. Taken together, our study compares the\r\ndifferent membrane designs across the tree of life and indicates how combining lipids can be\r\nused to resolve trade-offs when generating membranes for (bio)technological applications.\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Miguel full_name: Santana de Freitas Amaral, Miguel id: 4f2d02dd-47a9-11ec-ad10-82820ed3f501 last_name: Santana de Freitas Amaral citation: ama: 'Santana de Freitas Amaral M. Archaeal membranes : In silico modelling and design. 2024. doi:10.15479/at:ista:18661' apa: 'Santana de Freitas Amaral, M. (2024). Archaeal membranes : In silico modelling and design. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18661' chicago: 'Santana de Freitas Amaral, Miguel. “Archaeal Membranes : In Silico Modelling and Design.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18661.' ieee: 'M. Santana de Freitas Amaral, “Archaeal membranes : In silico modelling and design,” Institute of Science and Technology Austria, 2024.' ista: 'Santana de Freitas Amaral M. 2024. Archaeal membranes : In silico modelling and design. Institute of Science and Technology Austria.' mla: 'Santana de Freitas Amaral, Miguel. Archaeal Membranes : In Silico Modelling and Design. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18661.' short: 'M. Santana de Freitas Amaral, Archaeal Membranes : In Silico Modelling and Design, Institute of Science and Technology Austria, 2024.' corr_author: '1' date_created: 2024-12-16T10:53:39Z date_published: 2024-12-17T00:00:00Z date_updated: 2026-04-07T13:22:29Z day: '17' ddc: - '572' - '530' degree_awarded: PhD department: - _id: GradSch - _id: AnSa doi: 10.15479/at:ista:18661 file: - access_level: closed checksum: eca06497a29078558395455c890a32d9 content_type: application/zip creator: mamaral date_created: 2024-12-18T12:27:01Z date_updated: 2025-06-18T22:30:03Z embargo_to: open_access file_id: '18671' file_name: 2024_msfa_thesis.zip file_size: 19161387 relation: source_file - access_level: open_access checksum: 2dc30ea46c5daf48d07e4cccb3c3de00 content_type: application/pdf creator: mamaral date_created: 2024-12-18T12:26:30Z date_updated: 2025-06-18T22:30:03Z embargo: 2025-06-18 file_id: '18672' file_name: 2024_msfa_thesis.pdf file_size: 16530084 relation: main_file file_date_updated: 2025-06-18T22:30:03Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '57' publication_identifier: isbn: - 978-3-99078-046-6 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '18670' relation: part_of_dissertation status: public status: public supervisor: - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 title: 'Archaeal membranes : In silico modelling and design' tmp: image: /images/cc_by_sa.png legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0) short: CC BY-SA (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_place: repository _id: '18670' abstract: - lang: eng text: Across the tree of life, distinct designs of cellular membranes have evolved. In bacteria and eukaryotes single-headed lipids self-assemble into flexible bilayer membranes. By contrast, archaea often possess double-headed, monolayer spanning bolalipids, mixed with bilayer lipids, enabling them to survive in harsh environments. Here, using a minimal computational model for bolalipid membranes, we discover trade-offs when forming membranes. We find that membranes made out of flexible bolalipids resemble bilayer membranes as bolalipids exhibit conformational switch into U-shaped conformations to enable higher curvatures. Conversely, stiffer bolalipids, resembling those in extremophile archaea, take on straight conformations and form liquid membranes that are stiff, and prone to pore formation during membrane reshaping. Strikingly, we show how to achieve fluid bolalipid membranes that are both stable and flexible – by including small amounts of bilayer lipids, as archaea do. Our study explains how different organisms resolve trade-offs when generating membranes of desired material properties. acknowledgement: "MA, BB, and AŠ acknowledge funding by the\r\nVolkswagen Foundation Grant Az 96727. FF\r\nacknowledges fnancial support by the NOMIS\r\nfoundation. AŠ acknowledges funding by ERC\r\nStarting Grant “NEPA” 802960. We thank\r\nClaudia Flandoli for help with illustrations." article_processing_charge: No author: - first_name: Miguel full_name: Santana de Freitas Amaral, Miguel id: 4f2d02dd-47a9-11ec-ad10-82820ed3f501 last_name: Santana de Freitas Amaral - first_name: Felix F full_name: Frey, Felix F id: a0270b37-8f1a-11ec-95c7-8e710c59a4f3 last_name: Frey orcid: 0000-0001-8501-6017 - first_name: Xiuyun full_name: Jiang, Xiuyun last_name: Jiang - first_name: Buzz full_name: Baum, Buzz last_name: Baum - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 citation: ama: 'Santana de Freitas Amaral M, Frey FF, Jiang X, Baum B, Šarić A. Stability vs flexibility: Reshaping archaeal membranes in silico. bioRxiv. doi:10.1101/2024.10.18.619072' apa: 'Santana de Freitas Amaral, M., Frey, F. F., Jiang, X., Baum, B., & Šarić, A. (n.d.). Stability vs flexibility: Reshaping archaeal membranes in silico. bioRxiv. https://doi.org/10.1101/2024.10.18.619072' chicago: 'Santana de Freitas Amaral, Miguel, Felix F Frey, Xiuyun Jiang, Buzz Baum, and Anđela Šarić. “Stability vs Flexibility: Reshaping Archaeal Membranes in Silico.” BioRxiv, n.d. https://doi.org/10.1101/2024.10.18.619072.' ieee: 'M. Santana de Freitas Amaral, F. F. Frey, X. Jiang, B. Baum, and A. Šarić, “Stability vs flexibility: Reshaping archaeal membranes in silico,” bioRxiv. .' ista: 'Santana de Freitas Amaral M, Frey FF, Jiang X, Baum B, Šarić A. Stability vs flexibility: Reshaping archaeal membranes in silico. bioRxiv, 10.1101/2024.10.18.619072.' mla: 'Santana de Freitas Amaral, Miguel, et al. “Stability vs Flexibility: Reshaping Archaeal Membranes in Silico.” BioRxiv, doi:10.1101/2024.10.18.619072.' short: M. Santana de Freitas Amaral, F.F. Frey, X. Jiang, B. Baum, A. Šarić, BioRxiv (n.d.). corr_author: '1' date_created: 2024-12-18T10:07:45Z date_published: 2024-11-27T00:00:00Z date_updated: 2026-07-16T22:30:24Z day: '27' department: - _id: AnSa doi: 10.1101/2024.10.18.619072 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2024.10.18.619072 month: '11' oa: 1 oa_version: Preprint project: - _id: eba2549b-77a9-11ec-83b8-a81e493eae4e call_identifier: H2020 grant_number: '802960' name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines' publication: bioRxiv publication_status: draft related_material: record: - id: '18661' relation: dissertation_contains status: public status: public title: 'Stability vs flexibility: Reshaping archaeal membranes in silico' tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- APC_amount: 5887,8 EUR OA_place: publisher OA_type: hybrid _id: '15084' abstract: - lang: eng text: "GABAB receptor (GBR) activation inhibits neurotransmitter release in axon terminals in the brain, except in medial habenula (MHb) terminals, which show robust potentiation. However, mechanisms underlying this enigmatic potentiation remain elusive. Here, we report that GBR activation on MHb terminals induces an activity-dependent transition from a facilitating, tonic to a depressing, phasic neurotransmitter release mode. This transition is accompanied by a 4.1-fold increase in readily releasable vesicle pool (RRP) size and a 3.5-fold increase of docked synaptic vesicles (SVs) at the presynaptic active zone (AZ). Strikingly, the depressing phasic release exhibits looser coupling distance than the tonic release. Furthermore, the tonic and phasic release are selectively affected by deletion of synaptoporin (SPO) and Ca\r\n 2+\r\n -dependent activator protein for secretion 2 (CAPS2), respectively. SPO modulates augmentation, the short-term plasticity associated with tonic release, and CAPS2 retains the increased RRP for initial responses in phasic response trains. The cytosolic protein CAPS2 showed a SV-associated distribution similar to the vesicular transmembrane protein SPO, and they were colocalized in the same terminals. We developed the “Flash and Freeze-fracture” method, and revealed the release of SPO-associated vesicles in both tonic and phasic modes and activity-dependent recruitment of CAPS2 to the AZ during phasic release, which lasted several minutes. Overall, these results indicate that GBR activation translocates CAPS2 to the AZ along with the fusion of CAPS2-associated SVs, contributing to persistency of the RRP increase. Thus, we identified structural and molecular mechanisms underlying tonic and phasic neurotransmitter release and their transition by GBR activation in MHb terminals." acknowledged_ssus: - _id: M-Shop - _id: PreCl - _id: EM-Fac acknowledgement: We thank Erwin Neher and Ipe Ninan for critical comments on the manuscript. This project has received funding from the European Research Council (ERC) and European Commission, under the European Union’s Horizon 2020 research and innovation program (ERC grant agreement no. 694539 to R.S. and the Marie Skłodowska-Curie grant agreement no. 665385 to C.Ö.). This study was supported by the Cooperative Study Program of Center for Animal Resources and Collaborative Study of NINS. We thank Kohgaku Eguchi for statistical analysis, Yu Kasugai for additional EM imaging, Robert Beattie for the design of the slice recovery chamber for Flash and Freeze experiments, Todor Asenov from the ISTA machine shop for custom part preparations for high-pressure freezing, the ISTA preclinical facility for animal caretaking, and the ISTA EM facilities for technical support. article_number: e2301449121 article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Peter full_name: Koppensteiner, Peter id: 3B8B25A8-F248-11E8-B48F-1D18A9856A87 last_name: Koppensteiner orcid: 0000-0002-3509-1948 - first_name: Pradeep full_name: Bhandari, Pradeep id: 45EDD1BC-F248-11E8-B48F-1D18A9856A87 last_name: Bhandari orcid: 0000-0003-0863-4481 - first_name: Hüseyin C full_name: Önal, Hüseyin C id: 4659D740-F248-11E8-B48F-1D18A9856A87 last_name: Önal orcid: 0000-0002-2771-2011 - first_name: Carolina full_name: Borges Merjane, Carolina id: 4305C450-F248-11E8-B48F-1D18A9856A87 last_name: Borges Merjane orcid: 0000-0003-0005-401X - first_name: Elodie full_name: Le Monnier, Elodie id: 3B59276A-F248-11E8-B48F-1D18A9856A87 last_name: Le Monnier - first_name: Utsa full_name: Roy, Utsa id: 4d26cf11-5355-11ee-ae5a-eb05e255b9b2 last_name: Roy - first_name: Yukihiro full_name: Nakamura, Yukihiro last_name: Nakamura - first_name: Tetsushi full_name: Sadakata, Tetsushi last_name: Sadakata - first_name: Makoto full_name: Sanbo, Makoto last_name: Sanbo - first_name: Masumi full_name: Hirabayashi, Masumi last_name: Hirabayashi - first_name: JeongSeop full_name: Rhee, JeongSeop last_name: Rhee - first_name: Nils full_name: Brose, Nils last_name: Brose - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 citation: ama: Koppensteiner P, Bhandari P, Önal C, et al. GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(8). doi:10.1073/pnas.2301449121 apa: Koppensteiner, P., Bhandari, P., Önal, C., Borges Merjane, C., Le Monnier, E., Roy, U., … Shigemoto, R. (2024). GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2301449121 chicago: Koppensteiner, Peter, Pradeep Bhandari, Cihan Önal, Carolina Borges Merjane, Elodie Le Monnier, Utsa Roy, Yukihiro Nakamura, et al. “GABAB Receptors Induce Phasic Release from Medial Habenula Terminals through Activity-Dependent Recruitment of Release-Ready Vesicles.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2301449121. ieee: P. Koppensteiner et al., “GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 8. National Academy of Sciences, 2024. ista: Koppensteiner P, Bhandari P, Önal C, Borges Merjane C, Le Monnier E, Roy U, Nakamura Y, Sadakata T, Sanbo M, Hirabayashi M, Rhee J, Brose N, Jonas PM, Shigemoto R. 2024. GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles. Proceedings of the National Academy of Sciences of the United States of America. 121(8), e2301449121. mla: Koppensteiner, Peter, et al. “GABAB Receptors Induce Phasic Release from Medial Habenula Terminals through Activity-Dependent Recruitment of Release-Ready Vesicles.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 8, e2301449121, National Academy of Sciences, 2024, doi:10.1073/pnas.2301449121. short: P. Koppensteiner, P. Bhandari, C. Önal, C. Borges Merjane, E. Le Monnier, U. Roy, Y. Nakamura, T. Sadakata, M. Sanbo, M. Hirabayashi, J. Rhee, N. Brose, P.M. Jonas, R. Shigemoto, Proceedings of the National Academy of Sciences of the United States of America 121 (2024). corr_author: '1' date_created: 2024-03-05T09:23:55Z date_published: 2024-02-20T00:00:00Z date_updated: 2026-07-16T22:30:25Z day: '20' ddc: - '570' department: - _id: RySh - _id: PeJo doi: 10.1073/pnas.2301449121 ec_funded: 1 external_id: isi: - '001208567300006' pmid: - '38346189' file: - access_level: open_access checksum: b25b2a057c266ff317a48b0d54d6fc8a content_type: application/pdf creator: dernst date_created: 2024-03-12T13:42:42Z date_updated: 2024-03-12T13:42:42Z file_id: '15110' file_name: 2024_PNAS_Koppensteiner.pdf file_size: 13648221 relation: main_file success: 1 file_date_updated: 2024-03-12T13:42:42Z has_accepted_license: '1' intvolume: ' 121' isi: 1 issue: '8' language: - iso: eng month: '02' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 25CA28EA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694539' name: 'In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour' - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: Proceedings of the National Academy of Sciences of the United States of America publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' related_material: link: - description: News on ISTA Website relation: press_release url: https://ista.ac.at/en/news/neuronal-insights-flash-and-freeze-fracture/ record: - id: '13173' relation: research_data status: public - id: '19271' relation: dissertation_contains status: public scopus_import: '1' status: public title: GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 121 year: '2024' ... --- APC_amount: 3782,54 DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '17183' abstract: - lang: eng text: "The photon blockade breakdown in a continuously driven cavity QED system has been proposed as a prime example for a first-order driven-dissipative quantum phase transition. However, the predicted scaling from a microscopic behavior—dominated by quantum fluctuations—to a macroscopic one—characterized by stable phases—and the associated exponents and phase diagram have not been observed so far. In this work we couple a single transmon qubit with a fixed coupling strength \U0001D454 to a superconducting cavity that is in situ bandwidth \U0001D705 tunable to controllably approach this thermodynamic limit. Even though the system remains microscopic, we observe its behavior becoming increasingly macroscopic as a function of \U0001D454/\U0001D705. For the highest realized \U0001D454/\U0001D705 of approximately 287, the system switches with a characteristic timescale as long as 6 s between a bright coherent state with approximately 8×103 intracavity photons and the vacuum state. This exceeds the microscopic timescales by 6 orders of magnitude and approaches the perfect hysteresis expected between two macroscopic attractors in the thermodynamic limit. These findings and interpretation are qualitatively supported by neoclassical theory and large-scale quantum-jump Monte Carlo simulations. Besides shedding more light on driven-dissipative physics in the limit of strong light-matter coupling, this system might also find applications in quantum sensing and metrology." acknowledged_ssus: - _id: M-Shop acknowledgement: This work has received funding from the Austrian Science Fund (FWF) through BeyondC (F7105) and the European Union’s Horizon 2020 research and innovation program under Grant Agreement No. 862644 (FETopen QUARTET). A.V. acknowledges support from the National Research, Development and Innovation Office of Hungary (NKFIH) within the Quantum Information National Laboratory of Hungary. The authors thank the MIBA workshop and the Institute of Science and Technology Austria nanofabrication facility for technical support. We are grateful to HUN-REN Cloud for providing us with suitable computational infrastructure for the simulations. article_number: '010327' article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Riya full_name: Sett, Riya id: 2E6D040E-F248-11E8-B48F-1D18A9856A87 last_name: Sett orcid: 0000-0001-7641-8348 - first_name: Farid full_name: Hassani, Farid id: 2AED110C-F248-11E8-B48F-1D18A9856A87 last_name: Hassani orcid: 0000-0001-6937-5773 - first_name: Duc T full_name: Phan, Duc T id: 29C8C0B4-F248-11E8-B48F-1D18A9856A87 last_name: Phan - first_name: Shabir full_name: Barzanjeh, Shabir id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87 last_name: Barzanjeh orcid: 0000-0003-0415-1423 - first_name: Andras full_name: Vukics, Andras last_name: Vukics - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X citation: ama: Sett R, Hassani F, Phan DT, Barzanjeh S, Vukics A, Fink JM. Emergent macroscopic bistability induced by a single superconducting qubit. PRX Quantum. 2024;5(1). doi:10.1103/prxquantum.5.010327 apa: Sett, R., Hassani, F., Phan, D. T., Barzanjeh, S., Vukics, A., & Fink, J. M. (2024). Emergent macroscopic bistability induced by a single superconducting qubit. PRX Quantum. American Physical Society. https://doi.org/10.1103/prxquantum.5.010327 chicago: Sett, Riya, Farid Hassani, Duc T Phan, Shabir Barzanjeh, Andras Vukics, and Johannes M Fink. “Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.” PRX Quantum. American Physical Society, 2024. https://doi.org/10.1103/prxquantum.5.010327. ieee: R. Sett, F. Hassani, D. T. Phan, S. Barzanjeh, A. Vukics, and J. M. Fink, “Emergent macroscopic bistability induced by a single superconducting qubit,” PRX Quantum, vol. 5, no. 1. American Physical Society, 2024. ista: Sett R, Hassani F, Phan DT, Barzanjeh S, Vukics A, Fink JM. 2024. Emergent macroscopic bistability induced by a single superconducting qubit. PRX Quantum. 5(1), 010327. mla: Sett, Riya, et al. “Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.” PRX Quantum, vol. 5, no. 1, 010327, American Physical Society, 2024, doi:10.1103/prxquantum.5.010327. short: R. Sett, F. Hassani, D.T. Phan, S. Barzanjeh, A. Vukics, J.M. Fink, PRX Quantum 5 (2024). corr_author: '1' date_created: 2024-06-27T10:58:06Z date_published: 2024-02-16T00:00:00Z date_updated: 2026-07-16T22:30:27Z day: '16' ddc: - '530' department: - _id: JoFi - _id: AnHi doi: 10.1103/prxquantum.5.010327 ec_funded: 1 external_id: arxiv: - '2210.14182' isi: - '001171652500001' file: - access_level: open_access checksum: 0833880d47f74ad1deda93a1d8ffa5a7 content_type: application/pdf creator: cchlebak date_created: 2024-06-28T12:04:43Z date_updated: 2024-06-28T12:04:43Z file_id: '17185' file_name: 2024_PRXQuantum_Sett.pdf file_size: 1443351 relation: main_file success: 1 file_date_updated: 2024-06-28T12:04:43Z has_accepted_license: '1' intvolume: ' 5' isi: 1 issue: '1' language: - iso: eng month: '02' oa: 1 oa_version: Published Version project: - _id: 237CBA6C-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '862644' name: Quantum readout techniques and technologies - _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1 call_identifier: FWF name: FWF Open Access Fund - _id: bdb108fd-d553-11ed-ba76-83dc74a9864f grant_number: F07105 name: QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits publication: PRX Quantum publication_identifier: eissn: - 2691-3399 publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: record: - id: '18978' relation: research_data status: public - id: '19533' relation: dissertation_contains status: public scopus_import: '1' status: public title: Emergent macroscopic bistability induced by a single superconducting qubit tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2024' ... --- OA_place: repository OA_type: gold _id: '18978' abstract: - lang: eng text: "Data analysis files for the manuscript \"Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit\".\r\n\r\nThis contains the raw data and the data analysis files for generating the figures in the manuscript.\r\n\r\n Figure1 file - The raw data of cavity transmission spectra for 6 different kappas are there. They are fitted with input-output theory in the python file.\r\n Figure2 file - The raw data at 8 MHz kappa are included. all hte figures in figure 2 are generated in the python file\r\n Figure3 file - The raw data of PBB single shot measurements at all kappas are included. The detailed analysis and the Figure3 generated for the paper are all in the python analysis file. Also, thefiles containing the time-evolution of the intensity from Master Equation solution are included.\r\nFigure4 file - The raw data at 2.6 MHz for different drive detunings and the corresponding analyses are included. And the python file includes the analysis of the experimental data as well as approximate neoclassical equations solutions for 2-level and 3-level transmons are included. " article_processing_charge: No author: - first_name: Riya full_name: Sett, Riya id: 2E6D040E-F248-11E8-B48F-1D18A9856A87 last_name: Sett orcid: 0000-0001-7641-8348 - first_name: Farid full_name: Hassani, Farid id: 2AED110C-F248-11E8-B48F-1D18A9856A87 last_name: Hassani orcid: 0000-0001-6937-5773 - first_name: Duc T full_name: Phan, Duc T id: 29C8C0B4-F248-11E8-B48F-1D18A9856A87 last_name: Phan - first_name: Shabir full_name: Barzanjeh, Shabir id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87 last_name: Barzanjeh orcid: 0000-0003-0415-1423 - first_name: Andras full_name: Vukics, Andras last_name: Vukics - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X citation: ama: Sett R, Hassani F, Phan DT, Barzanjeh S, Vukics A, Fink JM. Data Analysis files for “Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.” 2024. doi:10.5281/ZENODO.10518320 apa: Sett, R., Hassani, F., Phan, D. T., Barzanjeh, S., Vukics, A., & Fink, J. M. (2024). Data Analysis files for “Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.” Zenodo. https://doi.org/10.5281/ZENODO.10518320 chicago: Sett, Riya, Farid Hassani, Duc T Phan, Shabir Barzanjeh, Andras Vukics, and Johannes M Fink. “Data Analysis Files for ‘Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.’” Zenodo, 2024. https://doi.org/10.5281/ZENODO.10518320. ieee: R. Sett, F. Hassani, D. T. Phan, S. Barzanjeh, A. Vukics, and J. M. Fink, “Data Analysis files for ‘Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.’” Zenodo, 2024. ista: Sett R, Hassani F, Phan DT, Barzanjeh S, Vukics A, Fink JM. 2024. Data Analysis files for ‘Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit’, Zenodo, 10.5281/ZENODO.10518320. mla: Sett, Riya, et al. Data Analysis Files for “Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit.” Zenodo, 2024, doi:10.5281/ZENODO.10518320. short: R. Sett, F. Hassani, D.T. Phan, S. Barzanjeh, A. Vukics, J.M. Fink, (2024). corr_author: '1' date_created: 2025-01-30T08:30:03Z date_published: 2024-01-16T00:00:00Z date_updated: 2026-07-16T22:30:27Z day: '16' ddc: - '530' department: - _id: JoFi - _id: AnHi doi: 10.5281/ZENODO.10518320 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.10518320 month: '01' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '17183' relation: used_in_publication status: public - id: '19533' relation: used_in_publication status: public status: public title: Data Analysis files for "Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit" tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '17148' abstract: - lang: eng text: During neural tube (NT) development, the notochord induces an organizer, the floorplate, which secretes Sonic Hedgehog (SHH) to pattern neural progenitors. Conversely, NT organoids (NTOs) from embryonic stem cells (ESCs) spontaneously form floorplates without the notochord, demonstrating that stem cells can self-organize without embryonic inducers. Here, we investigated floorplate self-organization in clonal mouse NTOs. Expression of the floorplate marker FOXA2 was initially spatially scattered before resolving into multiple clusters, which underwent competition and sorting, resulting in a stable “winning” floorplate. We identified that BMP signaling governed long-range cluster competition. FOXA2+ clusters expressed BMP4, suppressing FOXA2 in receiving cells while simultaneously expressing the BMP-inhibitor NOGGIN, promoting cluster persistence. Noggin mutation perturbed floorplate formation in NTOs and in the NT in vivo at mid/hindbrain regions, demonstrating how the floorplate can form autonomously without the notochord. Identifying the pathways governing organizer self-organization is critical for harnessing the developmental plasticity of stem cells in tissue engineering. acknowledgement: We thank P. Pasierbek, A.C. Moreno, T. Lendl, and K. Aumayr for microscopy support; G. Schmauss for FACS support; M. Novatchkova for assistance with Bioinformatic analyses; J. Ahel, A. Polikarpova, S. Horer, E. Cesare, and E. Norouzi for technical assistance; A. Meinhardt for supervision; DRESDEN-concept Genome Center, A. Vogt, A. Sommer, and the Vienna BioCenter NGS facility for RNA sequencing. We are grateful to M. Placzek and E. Martí for discussions about the floorplate; to S. Shvartsman for valuable input; to A. Aszodi, W. Masselink, and S. Raiders for advice on statistical analyses; to J. Cornwall Scoones, G. Martello, and Tanaka lab members for critical reading of the manuscript; E. Bassat and E. Chatzidaki for contributing schematics; and to K. Lust for support. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement ERC AdG 742046) to E.M.T. This research was funded in whole or in part by the Austrian Science Fund (FWF) (10.55776/F7803-B) (Stem Cell Modulation) to E.M.T. and A.K., Sir Henry Wellcome postdoctoral fellowship to H.T.S., ELBE fellowship to K.I., and National Science Foundation (US) Phy 2013131 to E.S. The A.K. lab is also supported by ISTA and the European Research Council under Horizon Europe grant 101044579, and S.L. is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011. This work was supported in part by the Francis Crick Institute, which receives its core funding from Cancer Research UK (CC001051), the UK Medical Research Council (CC001051), and the Wellcome Trust (CC001051). For the purpose of open access, the authors have applied a CC BY public copyright license to any author accepted manuscript (AAM) version arising from this submission. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Teresa full_name: Krammer, Teresa last_name: Krammer - first_name: Hannah T. full_name: Stuart, Hannah T. last_name: Stuart - first_name: Elena full_name: Gromberg, Elena last_name: Gromberg - first_name: Keisuke full_name: Ishihara, Keisuke last_name: Ishihara - first_name: Dillon full_name: Cislo, Dillon last_name: Cislo - first_name: Manuela full_name: Melchionda, Manuela last_name: Melchionda - first_name: Fernando full_name: Becerril Perez, Fernando last_name: Becerril Perez - first_name: Jingkui full_name: Wang, Jingkui last_name: Wang - first_name: Elena full_name: Costantini, Elena last_name: Costantini - first_name: Stefanie full_name: Rus, Stefanie id: 4D9EC9B6-F248-11E8-B48F-1D18A9856A87 last_name: Rus orcid: 0000-0001-8703-1093 - first_name: Laura full_name: Arbanas, Laura last_name: Arbanas - first_name: Alexandra full_name: Hörmann, Alexandra last_name: Hörmann - first_name: Ralph A. full_name: Neumüller, Ralph A. last_name: Neumüller - first_name: Nicola full_name: Elvassore, Nicola last_name: Elvassore - first_name: Eric full_name: Siggia, Eric last_name: Siggia - first_name: James full_name: Briscoe, James last_name: Briscoe - first_name: Anna full_name: Kicheva, Anna id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 - first_name: Elly M. full_name: Tanaka, Elly M. last_name: Tanaka citation: ama: Krammer T, Stuart HT, Gromberg E, et al. Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition. Developmental Cell. 2024;59(15):1940-1953.e10. doi:10.1016/j.devcel.2024.04.021 apa: Krammer, T., Stuart, H. T., Gromberg, E., Ishihara, K., Cislo, D., Melchionda, M., … Tanaka, E. M. (2024). Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2024.04.021 chicago: Krammer, Teresa, Hannah T. Stuart, Elena Gromberg, Keisuke Ishihara, Dillon Cislo, Manuela Melchionda, Fernando Becerril Perez, et al. “Mouse Neural Tube Organoids Self-Organize Floorplate through BMP-Mediated Cluster Competition.” Developmental Cell. Elsevier, 2024. https://doi.org/10.1016/j.devcel.2024.04.021. ieee: T. Krammer et al., “Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition,” Developmental Cell, vol. 59, no. 15. Elsevier, p. 1940–1953.e10, 2024. ista: Krammer T, Stuart HT, Gromberg E, Ishihara K, Cislo D, Melchionda M, Becerril Perez F, Wang J, Costantini E, Rus S, Arbanas L, Hörmann A, Neumüller RA, Elvassore N, Siggia E, Briscoe J, Kicheva A, Tanaka EM. 2024. Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition. Developmental Cell. 59(15), 1940–1953.e10. mla: Krammer, Teresa, et al. “Mouse Neural Tube Organoids Self-Organize Floorplate through BMP-Mediated Cluster Competition.” Developmental Cell, vol. 59, no. 15, Elsevier, 2024, p. 1940–1953.e10, doi:10.1016/j.devcel.2024.04.021. short: T. Krammer, H.T. Stuart, E. Gromberg, K. Ishihara, D. Cislo, M. Melchionda, F. Becerril Perez, J. Wang, E. Costantini, S. Rus, L. Arbanas, A. Hörmann, R.A. Neumüller, N. Elvassore, E. Siggia, J. Briscoe, A. Kicheva, E.M. Tanaka, Developmental Cell 59 (2024) 1940–1953.e10. date_created: 2024-06-16T22:01:07Z date_published: 2024-08-01T00:00:00Z date_updated: 2026-07-16T22:30:29Z day: '01' ddc: - '570' department: - _id: AnKi doi: 10.1016/j.devcel.2024.04.021 external_id: isi: - '001289684800001' pmid: - '38776925' file: - access_level: open_access checksum: fefdea9c02862b4bb74de49b65ce638a content_type: application/pdf creator: dernst date_created: 2025-01-13T10:59:12Z date_updated: 2025-01-13T10:59:12Z file_id: '18841' file_name: 2024_DevelopmentalCell_Krammer.pdf file_size: 6249076 relation: main_file success: 1 file_date_updated: 2025-01-13T10:59:12Z has_accepted_license: '1' intvolume: ' 59' isi: 1 issue: '15' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: 1940-1953.e10 pmid: 1 project: - _id: bd7e737f-d553-11ed-ba76-d69ffb5ee3aa grant_number: '101044579' name: Mechanisms of tissue size regulation in spinal cord development - _id: 9B9B39FA-BA93-11EA-9121-9846C619BF3A grant_number: SC19-011 name: The regulatory logic of pattern formation in the vertebrate dorsal neural tube publication: Developmental Cell publication_identifier: eissn: - 1878-1551 issn: - 1534-5807 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '19763' relation: dissertation_contains status: public scopus_import: '1' status: public title: Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 59 year: '2024' ... --- APC_amount: 804 EUR DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '18601' abstract: - lang: eng text: "Geometrically controlled stem cell differentiation promotes reproducible pattern formation. Here, we present a protocol to fabricate elastomeric stencils for patterned stem cell differentiation. We describe procedures for using photolithography to produce molds, followed by molding polydimethylsiloxane (PDMS) to obtain stencils with through holes. We then provide instructions for culturing cells on stencils and, finally, removing stencils to allow colony growth and cell migration. This approach yields reproducible two-dimensional organoids tailored for quantitative studies of growth and pattern formation.\r\nFor complete details on the use and execution of this protocol, please refer to Lehr et al.1" acknowledged_ssus: - _id: NanoFab acknowledgement: We thank the nanofabrication facility at ISTA for technical assistance. Work in the A.K. lab is supported by ISTA, the European Research Council under Horizon Europe (grant 101044579), and the Austrian Science Fund (FWF) (grant https://doi.org/10.55776/F78). S.L. is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011. article_number: '103187' article_processing_charge: Yes article_type: original author: - first_name: Stefanie full_name: Rus, Stefanie id: 4D9EC9B6-F248-11E8-B48F-1D18A9856A87 last_name: Rus orcid: 0000-0001-8703-1093 - first_name: Jack full_name: Merrin, Jack id: 4515C308-F248-11E8-B48F-1D18A9856A87 last_name: Merrin orcid: 0000-0001-5145-4609 - first_name: Monika Aleksandra full_name: Kulig, Monika Aleksandra id: 3331f5ae-e896-11ec-af79-eeb79769bcb7 last_name: Kulig - first_name: Thomas full_name: Minchington, Thomas id: 7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f last_name: Minchington - first_name: Anna full_name: Kicheva, Anna id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 citation: ama: Rus S, Merrin J, Kulig MA, Minchington T, Kicheva A. Protocol for fabricating elastomeric stencils for patterned stem cell differentiation. STAR Protocols. 2024;5(4). doi:10.1016/j.xpro.2024.103187 apa: Rus, S., Merrin, J., Kulig, M. A., Minchington, T., & Kicheva, A. (2024). Protocol for fabricating elastomeric stencils for patterned stem cell differentiation. STAR Protocols. Elsevier. https://doi.org/10.1016/j.xpro.2024.103187 chicago: Rus, Stefanie, Jack Merrin, Monika Aleksandra Kulig, Thomas Minchington, and Anna Kicheva. “Protocol for Fabricating Elastomeric Stencils for Patterned Stem Cell Differentiation.” STAR Protocols. Elsevier, 2024. https://doi.org/10.1016/j.xpro.2024.103187. ieee: S. Rus, J. Merrin, M. A. Kulig, T. Minchington, and A. Kicheva, “Protocol for fabricating elastomeric stencils for patterned stem cell differentiation,” STAR Protocols, vol. 5, no. 4. Elsevier, 2024. ista: Rus S, Merrin J, Kulig MA, Minchington T, Kicheva A. 2024. Protocol for fabricating elastomeric stencils for patterned stem cell differentiation. STAR Protocols. 5(4), 103187. mla: Rus, Stefanie, et al. “Protocol for Fabricating Elastomeric Stencils for Patterned Stem Cell Differentiation.” STAR Protocols, vol. 5, no. 4, 103187, Elsevier, 2024, doi:10.1016/j.xpro.2024.103187. short: S. Rus, J. Merrin, M.A. Kulig, T. Minchington, A. Kicheva, STAR Protocols 5 (2024). corr_author: '1' date_created: 2024-12-01T23:01:53Z date_published: 2024-12-20T00:00:00Z date_updated: 2026-07-16T22:30:29Z day: '20' ddc: - '570' department: - _id: AnKi - _id: NanoFab doi: 10.1016/j.xpro.2024.103187 external_id: pmid: - '39602310' file: - access_level: open_access checksum: 0c61a6f9978608a103865905e06f4581 content_type: application/pdf creator: dernst date_created: 2024-12-03T10:53:23Z date_updated: 2024-12-03T10:53:23Z file_id: '18610' file_name: 2024_STARProtoc_Lehr.pdf file_size: 4989169 relation: main_file success: 1 file_date_updated: 2024-12-03T10:53:23Z has_accepted_license: '1' intvolume: ' 5' issue: '4' language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 project: - _id: bd7e737f-d553-11ed-ba76-d69ffb5ee3aa grant_number: '101044579' name: Mechanisms of tissue size regulation in spinal cord development - _id: 9B9B39FA-BA93-11EA-9121-9846C619BF3A grant_number: SC19-011 name: The regulatory logic of pattern formation in the vertebrate dorsal neural tube publication: STAR Protocols publication_identifier: eissn: - 2666-1667 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '19763' relation: dissertation_contains status: public scopus_import: '1' status: public title: Protocol for fabricating elastomeric stencils for patterned stem cell differentiation tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2024' ... --- OA_place: repository OA_type: green _id: '14796' abstract: - lang: eng text: Key innovations are fundamental to biological diversification, but their genetic basis is poorly understood. A recent transition from egg-laying to live-bearing in marine snails (Littorina spp.) provides the opportunity to study the genetic architecture of an innovation that has evolved repeatedly across animals. Individuals do not cluster by reproductive mode in a genome-wide phylogeny, but local genealogical analysis revealed numerous small genomic regions where all live-bearers carry the same core haplotype. Candidate regions show evidence for live-bearer–specific positive selection and are enriched for genes that are differentially expressed between egg-laying and live-bearing reproductive systems. Ages of selective sweeps suggest that live-bearer–specific alleles accumulated over more than 200,000 generations. Our results suggest that new functions evolve through the recruitment of many alleles rather than in a single evolutionary step. acknowledgement: "We thank J. Galindo, M. Montaño-Rendón, N. Mikhailova, A. Blakeslee, E. Arnason, and P. Kemppainen for providing samples; R. Turney, G. Sotelo, J. Larsson, T. Broquet, and S. Loisel for help collecting samples; Science Animated for providing the snail cartoons shown in Fig. 1; M. Dunning for help in developing bioinformatic pipelines; R. Faria, H. Morales, and V. Sousa for advice; and M. Hahn, J. Slate, M. Ravinet, J. Raeymaekers, A. Comeault, and N. Barton for feedback on a draft manuscript.\r\nThis work was supported by the Natural Environment Research Council (grant NE/P001610/1 to R.K.B.), the European Research Council (grant ERC-2015-AdG693030-BARRIERS to R.K.B.), the Norwegian Research Council (RCN Project 315287 to A.M.W.), and the Swedish Research Council (grant 2020-05385 to E.L.)." article_processing_charge: No article_type: original author: - first_name: Sean full_name: Stankowski, Sean id: 43161670-5719-11EA-8025-FABC3DDC885E last_name: Stankowski - first_name: Zuzanna B. full_name: Zagrodzka, Zuzanna B. last_name: Zagrodzka - first_name: Martin D. full_name: Garlovsky, Martin D. last_name: Garlovsky - first_name: Arka full_name: Pal, Arka id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425 last_name: Pal orcid: 0000-0002-4530-8469 - first_name: Daria full_name: Shipilina, Daria id: 428A94B0-F248-11E8-B48F-1D18A9856A87 last_name: Shipilina orcid: 0000-0002-1145-9226 - first_name: Diego Fernando full_name: Garcia Castillo, Diego Fernando id: ae681a14-dc74-11ea-a0a7-c6ef18161701 last_name: Garcia Castillo - first_name: Hila full_name: Lifchitz, Hila id: d6ab5470-2fb3-11ed-8633-986a9b84edac last_name: Lifchitz - first_name: Alan full_name: Le Moan, Alan last_name: Le Moan - first_name: Erica full_name: Leder, Erica last_name: Leder - first_name: James full_name: Reeve, James last_name: Reeve - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Roger K. full_name: Butlin, Roger K. last_name: Butlin citation: ama: Stankowski S, Zagrodzka ZB, Garlovsky MD, et al. The genetic basis of a recent transition to live-bearing in marine snails. Science. 2024;383(6678):114-119. doi:10.1126/science.adi2982 apa: Stankowski, S., Zagrodzka, Z. B., Garlovsky, M. D., Pal, A., Shipilina, D., Garcia Castillo, D. F., … Butlin, R. K. (2024). The genetic basis of a recent transition to live-bearing in marine snails. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.adi2982 chicago: Stankowski, Sean, Zuzanna B. Zagrodzka, Martin D. Garlovsky, Arka Pal, Daria Shipilina, Diego Fernando Garcia Castillo, Hila Lifchitz, et al. “The Genetic Basis of a Recent Transition to Live-Bearing in Marine Snails.” Science. American Association for the Advancement of Science, 2024. https://doi.org/10.1126/science.adi2982. ieee: S. Stankowski et al., “The genetic basis of a recent transition to live-bearing in marine snails,” Science, vol. 383, no. 6678. American Association for the Advancement of Science, pp. 114–119, 2024. ista: Stankowski S, Zagrodzka ZB, Garlovsky MD, Pal A, Shipilina D, Garcia Castillo DF, Lifchitz H, Le Moan A, Leder E, Reeve J, Johannesson K, Westram AM, Butlin RK. 2024. The genetic basis of a recent transition to live-bearing in marine snails. Science. 383(6678), 114–119. mla: Stankowski, Sean, et al. “The Genetic Basis of a Recent Transition to Live-Bearing in Marine Snails.” Science, vol. 383, no. 6678, American Association for the Advancement of Science, 2024, pp. 114–19, doi:10.1126/science.adi2982. short: S. Stankowski, Z.B. Zagrodzka, M.D. Garlovsky, A. Pal, D. Shipilina, D.F. Garcia Castillo, H. Lifchitz, A. Le Moan, E. Leder, J. Reeve, K. Johannesson, A.M. Westram, R.K. Butlin, Science 383 (2024) 114–119. corr_author: '1' date_created: 2024-01-14T23:00:56Z date_published: 2024-01-05T00:00:00Z date_updated: 2026-07-16T22:30:38Z day: '05' department: - _id: NiBa - _id: GradSch doi: 10.1126/science.adi2982 external_id: isi: - '001138156400003' pmid: - '38175895' intvolume: ' 383' isi: 1 issue: '6678' language: - iso: eng main_file_link: - open_access: '1' url: https://figshare.com/articles/journal_contribution/The_genetic_basis_of_a_recent_transition_to_live-bearing_in_marine_snails/26356054?file=47868241 month: '01' oa: 1 oa_version: Submitted Version page: 114-119 pmid: 1 publication: Science publication_identifier: eissn: - 1095-9203 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' related_material: link: - description: News on ISTA Website relation: press_release url: https://ista.ac.at/en/news/the-snail-or-the-egg/ record: - id: '14812' relation: research_data status: public - id: '20694' relation: dissertation_contains status: public scopus_import: '1' status: public title: The genetic basis of a recent transition to live-bearing in marine snails type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 383 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '18706' abstract: - lang: eng text: "We prove discrete-to-continuum convergence for dynamical optimal transport on Zd\r\n -periodic graphs with cost functional having linear growth at infinity. This result provides an answer to a problem left open by Gladbach, Kopfer, Maas, and Portinale (Calc Var Partial Differential Equations 62(5), 2023), where the convergence behaviour of discrete boundary-value dynamical transport problems is proved under the stronger assumption of superlinear growth. Our result extends the known literature to some important classes of examples, such as scaling limits of 1 -Wasserstein transport problems. Similarly to what happens in the quadratic case, the geometry of the graph plays a crucial role in the structure of the limit cost function, as we discuss in the final part of this work, which includes some visual representations." acknowledgement: L.P. gratefully acknowledges fundings from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – GZ 2047/1, Projekt-ID 390685813. F.Q. gratefully acknowledges support from the Austrian Science Fund (FWF) project 10.55776/F65. article_processing_charge: Yes article_type: original author: - first_name: Lorenzo full_name: Portinale, Lorenzo id: 30AD2CBC-F248-11E8-B48F-1D18A9856A87 last_name: Portinale - first_name: Filippo full_name: Quattrocchi, Filippo id: 3ebd6ba8-edfb-11eb-afb5-91a9745ba308 last_name: Quattrocchi orcid: 0009-0000-9773-1931 citation: ama: Portinale L, Quattrocchi F. Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs. European Journal of Applied Mathematics. 2024:1-29. doi:10.1017/s0956792524000810 apa: Portinale, L., & Quattrocchi, F. (2024). Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs. European Journal of Applied Mathematics. Cambridge University Press. https://doi.org/10.1017/s0956792524000810 chicago: Portinale, Lorenzo, and Filippo Quattrocchi. “Discrete-to-Continuum Limits of Optimal Transport with Linear Growth on Periodic Graphs.” European Journal of Applied Mathematics. Cambridge University Press, 2024. https://doi.org/10.1017/s0956792524000810. ieee: L. Portinale and F. Quattrocchi, “Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs,” European Journal of Applied Mathematics. Cambridge University Press, pp. 1–29, 2024. ista: Portinale L, Quattrocchi F. 2024. Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs. European Journal of Applied Mathematics., 1–29. mla: Portinale, Lorenzo, and Filippo Quattrocchi. “Discrete-to-Continuum Limits of Optimal Transport with Linear Growth on Periodic Graphs.” European Journal of Applied Mathematics, Cambridge University Press, 2024, pp. 1–29, doi:10.1017/s0956792524000810. short: L. Portinale, F. Quattrocchi, European Journal of Applied Mathematics (2024) 1–29. date_created: 2024-12-23T11:03:59Z date_published: 2024-12-20T00:00:00Z date_updated: 2026-07-16T22:30:39Z day: '20' ddc: - '500' department: - _id: GradSch - _id: JaMa doi: 10.1017/s0956792524000810 external_id: isi: - '001381435800001' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1017/S0956792524000810 month: '12' oa: 1 oa_version: Published Version page: 1-29 project: - _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2 grant_number: F6504 name: Taming Complexity in Partial Differential Systems publication: European Journal of Applied Mathematics publication_identifier: eissn: - 1469-4425 issn: - 0956-7925 publication_status: epub_ahead publisher: Cambridge University Press quality_controlled: '1' related_material: record: - id: '20563' relation: dissertation_contains status: public scopus_import: '1' status: public title: Discrete-to-continuum limits of optimal transport with linear growth on periodic graphs type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: repository OA_type: green _id: '20571' abstract: - lang: eng text: "We prove the convergence of a modified Jordan--Kinderlehrer--Otto scheme to a solution to the Fokker--Planck equation in $\\Omega \\Subset \\mathbb{R}^d$ with general, positive and temporally constant, Dirichlet boundary conditions. We work under mild assumptions on the domain, the drift, and the initial datum. \ In the special case where $\\Omega$ is an interval in $\\mathbb{R}^1$, we prove that such a solution is a gradient flow -- curve of maximal slope -- within a suitable space of measures, endowed with a modified Wasserstein distance.\r\nOur discrete scheme and modified distance draw inspiration from contributions by A. Figalli and N. Gigli [J. Math. Pures Appl. 94, (2010), pp. 107--130], and J. Morales [J. Math. Pures Appl. 112, (2018), pp. 41--88] on an optimal-transport approach to evolution equations with Dirichlet boundary conditions. Similarly to these works, we allow the mass to flow from/to the boundary $\\partial \\Omega$ throughout the evolution. However, our leading idea is to also keep track of the mass at the boundary by working with measures defined on the whole closure $\\overline \\Omega$. The driving functional is a modification of the classical relative entropy that also makes use of the information at the boundary. As an intermediate result, when $\\Omega$ is an interval in $\\mathbb{R}^1$, we find a formula for the descending slope of this geodesically nonconvex functional. " acknowledgement: "The author would like to thank Jan Maas for suggesting this project and for many helpful\r\ncomments, Antonio Agresti, Lorenzo Dello Schiavo and Julian Fischer for several fruitful discussions, and Oliver Tse for pointing out the reference [15]. He also gratefully acknowledges support from the Austrian Science Fund (FWF) project 10.55776/F65.\r\n" article_number: '2403.07803' article_processing_charge: No arxiv: 1 author: - first_name: Filippo full_name: Quattrocchi, Filippo id: 3ebd6ba8-edfb-11eb-afb5-91a9745ba308 last_name: Quattrocchi orcid: 0009-0000-9773-1931 citation: ama: Quattrocchi F. Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions. arXiv. doi:10.48550/arXiv.2403.07803 apa: Quattrocchi, F. (n.d.). Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions. arXiv. https://doi.org/10.48550/arXiv.2403.07803 chicago: Quattrocchi, Filippo. “Variational Structures for the Fokker-Planck Equation with General Dirichlet Boundary Conditions.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2403.07803. ieee: F. Quattrocchi, “Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions,” arXiv. . ista: Quattrocchi F. Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions. arXiv, 2403.07803. mla: Quattrocchi, Filippo. “Variational Structures for the Fokker-Planck Equation with General Dirichlet Boundary Conditions.” ArXiv, 2403.07803, doi:10.48550/arXiv.2403.07803. short: F. Quattrocchi, ArXiv (n.d.). corr_author: '1' date_created: 2025-10-28T13:12:56Z date_published: 2024-04-09T00:00:00Z date_updated: 2026-07-16T22:30:39Z day: '09' department: - _id: GradSch - _id: JaMa doi: 10.48550/arXiv.2403.07803 external_id: arxiv: - '2403.07803' keyword: - gradient flows - Jordan–Kinderlehrer–Otto scheme - curves of maximal slope - optimal transport - Dirichlet boundary conditions - Fokker–Planck equation language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2403.07803 month: '04' oa: 1 oa_version: Preprint project: - _id: 260482E2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: F06504 name: Taming Complexity in Partial Differential Systems publication: arXiv publication_status: draft related_material: record: - id: '20865' relation: later_version status: public - id: '20563' relation: dissertation_contains status: public status: public title: Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: repository OA_type: green _id: '20570' abstract: - lang: eng text: "We investigate the minimal error in approximating a general probability\r\nmeasure $\\mu$ on $\\mathbb{R}^d$ by the uniform measure on a finite set with\r\nprescribed cardinality $n$. The error is measured in the $p$-Wasserstein\r\ndistance. In particular, when $1\\le parXiv. doi:10.48550/arXiv.2408.12924 apa: Quattrocchi, F. (n.d.). Asymptotics for optimal empirical quantization of measures. arXiv. https://doi.org/10.48550/arXiv.2408.12924 chicago: Quattrocchi, Filippo. “Asymptotics for Optimal Empirical Quantization of Measures.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2408.12924. ieee: F. Quattrocchi, “Asymptotics for optimal empirical quantization of measures,” arXiv. . ista: Quattrocchi F. Asymptotics for optimal empirical quantization of measures. arXiv, 2408.12924. mla: Quattrocchi, Filippo. “Asymptotics for Optimal Empirical Quantization of Measures.” ArXiv, 2408.12924, doi:10.48550/arXiv.2408.12924. short: F. Quattrocchi, ArXiv (n.d.). corr_author: '1' date_created: 2025-10-28T13:12:22Z date_published: 2024-08-23T00:00:00Z date_updated: 2026-07-16T22:30:39Z day: '23' department: - _id: GradSch - _id: JaMa doi: 10.48550/arXiv.2408.12924 external_id: arxiv: - '2408.12924' keyword: - optimal empirical quantization - vector quantization - Wasserstein distance - semidiscrete optimal transport - Zador’s Theorem - Pierce’s Lemma language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2408.12924 month: '08' oa: 1 oa_version: Preprint project: - _id: 260482E2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: F06504 name: Taming Complexity in Partial Differential Systems publication: arXiv publication_status: draft related_material: record: - id: '20563' relation: dissertation_contains status: public status: public title: Asymptotics for optimal empirical quantization of measures type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: publisher _id: '17206' abstract: - lang: eng text: "Males and females exhibit numerous differences, from the initial stages of sex determination to the\r\ndevelopment of secondary sexual characteristics. In Drosophila, these differences have been\r\nthoroughly studied. Extensive research has been performed to understand the role and molecular\r\nmode of action of central sex in determining switch genes, such as transformer (tra) and Sex-lethal\r\n(Sxl). Furthermore, studies have highlighted differential gene expression as an essential mechanism to\r\ncreate sexual dimorphism. An alternative path to sexual dimorphism that has been less explored is\r\nalternative splicing, the mechanism through which genes can produce multiple transcripts with\r\ndistinct properties and functions. The primary switch sex-determining gene Sxl is a good example of\r\nthe role of alternative splicing for sex-specific functions: the inclusion of a specific exon determines\r\nthe male or female form of the protein, which in turn switches on either the male or female\r\ndevelopmental pathway. The genes that act upstream of Sxl and determine which form is expressed -\r\nthe counter genes - have received less attention. This thesis addresses two critical questions about\r\nthe molecular encoding of sexes in the Drosophila melanogaster genome: First, the use of splice forms\r\nin male and female tissues in D. melanogaster is examined, inferring the molecular and evolutionary\r\nparameters shaping the diversity of the splicing landscape. Second, the behaviour of counter genes in\r\nDrosophila-related species is investigated, shedding light on potential changes leading to their\r\nincorporation into the sex-determination pathway.\r\nFor the alternative splicing analyses, long-read RNA sequencing of testes, ovaries, female and male\r\nmidguts, heads, and whole bodies was performed. A novel pipeline was developed to assign unique\r\ntranscript identifiers for each sequence of exons and introns in the read, enabling detailed\r\ncomparisons of splicing variants in each tissue/sex. Alternative splicing was found to be more\r\npervasive in females than males (22,201 exclusive splice forms in females versus 12,631 in males),\r\nespecially when comparing ovaries to other tissues. The ovaries alone displayed 15,299 exclusive\r\nsplice forms, suggesting most female exclusive splice forms originate there. Genome location and gene\r\nage were also correlated with the number of splice forms per gene. In particular, the X and 4th\r\nchromosomes (Muller elements A and F) showed more splice forms per gene than other\r\nchromosomes. Additionally, genes older than 63 million years exhibited more splice forms per gene\r\nthan younger genes. Our results suggest that alternative splicing is more prevalent than previously\r\nbelieved, with numerous female-exclusive forms, age, and location playing significant roles in shaping\r\nits prevalence.\r\nFor the counter genes analyses, we combined published gene expression, genomic, and gene\r\ninteraction data from various clades (Bactrocera jarvisi, B. oleae, Ceratitis capitata, Mus musculus,\r\nCaenorhabditis elegans, Homo sapiens, and D. melanogaster). The counter genes scute (sc), extra\r\nmacrochaetae (emc), groucho (gro), deadpan (dpn), daughterless (da), runt (run), Sxl, hermaphrodite\r\n(her), and tra maintain conserved Muller element locations between C. capitata and D. melanogaster,\r\nwhich are most of the counter genes identified in the C. capitata genome. Their expression patterns\r\nduring early embryogenesis in B. jarvisi and D. melanogaster are also similar for counter genes dpn,\r\ngro, da, and emc. However, Sxl and sc are also found to have more extreme expression ratios between\r\nthe species. Lastly, gene interactions within the counter genes are conserved, with da-sc and gro-dpn\r\ninteractions occurring in Drosophila, worms, humans, and mice. Interactions such as dpn-sc, dpn-da,\r\nda-emc, and gro-run are present in Drosophila, mice, and humans, suggesting these genes were\r\nrecruited by ancestral characteristics, primarily during embryogenesis. The conserved expression,\r\nlocation, and interactions of counter genes suggest serendipitous recruitment of such genes instead\r\nof a change in those characteristics as they were recruited for this function. " acknowledged_ssus: - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Julia full_name: Raices, Julia id: 3EE67F22-F248-11E8-B48F-1D18A9856A87 last_name: Raices citation: ama: 'Raices J. Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination. 2024. doi:10.15479/at:ista:17206' apa: 'Raices, J. (2024). Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17206' chicago: 'Raices, Julia. “Novel Approaches to Studying Alternative Splicing in Drosophila Melanogaster : Insights into Sex-Specific Gene Expression and the Evolution of Sex Determination.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17206.' ieee: 'J. Raices, “Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination,” Institute of Science and Technology Austria, 2024.' ista: 'Raices J. 2024. Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination. Institute of Science and Technology Austria.' mla: 'Raices, Julia. Novel Approaches to Studying Alternative Splicing in Drosophila Melanogaster : Insights into Sex-Specific Gene Expression and the Evolution of Sex Determination. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17206.' short: 'J. Raices, Novel Approaches to Studying Alternative Splicing in Drosophila Melanogaster : Insights into Sex-Specific Gene Expression and the Evolution of Sex Determination, Institute of Science and Technology Austria, 2024.' corr_author: '1' date_created: 2024-07-05T14:15:29Z date_published: 2024-07-05T00:00:00Z date_updated: 2026-04-07T13:03:22Z day: '05' ddc: - '570' degree_awarded: PhD department: - _id: BeVi - _id: GradSch doi: 10.15479/at:ista:17206 ec_funded: 1 file: - access_level: closed checksum: d5e9234bde8667b005a8cfe18bb467d3 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: cchlebak date_created: 2024-07-11T07:18:01Z date_updated: 2025-01-11T23:30:04Z embargo_to: open_access file_id: '17223' file_name: ThesisRaices2024_postDefense.docx file_size: 13788479 relation: source_file - access_level: open_access checksum: f5ed0139aa3e11ce58369f0915647c5c content_type: application/pdf creator: cchlebak date_created: 2024-07-11T07:22:32Z date_updated: 2025-01-11T23:30:04Z embargo: 2025-01-11 file_id: '17224' file_name: ThesisRaices2024_nosignature.pdf file_size: 5580296 relation: main_file file_date_updated: 2025-01-11T23:30:04Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '82' project: - _id: 250BDE62-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715257' name: Prevalence and Influence of Sexual Antagonism on Genome Evolution publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 title: 'Novel approaches to studying alternative splicing in Drosophila Melanogaster : Insights into sex-specific gene expression and the evolution of sex determination' tmp: image: /images/cc_by_sa.png legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0) short: CC BY-SA (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_place: publisher _id: '18101' abstract: - lang: eng text: "The Retroviridae family consists of two sub-families, the Orthoretrovirinae and the\r\nSpumaretrovirinae. The Orthoretroviruses contain important human pathogens, such as the\r\nhuman immunodeficiency virus 1 (HIV-1). They also harbor other retrovirus species which\r\nare regularly used as model systems to study the retroviral life cycle. The main structural\r\ncomponent of the retroviruses, is the Gag protein and its truncation derivatives occurring\r\nduring viral maturation. Orthoretroviral Gag assemblies have been extensively studied to\r\nunderstand the interactions that confer stability and morphology to viral particles.\r\nThe Spumaretrovirinae subfamily represent an early diverging branch of the Retroviridae.\r\nIts members, the Foamy viruses (FV), share most of the conventional features found in\r\nretroviruses. However, they also possess multiple characteristics that make them unique. In\r\nparticular, FV Gag does not get extensively cleaved as in orthoretroviruses. Hence, the Gag\r\narchitecture deviates from the canonical domain arrangement in FV. They also exhibit a\r\npeculiar particle morphology, having no apparent immature state and a seemingly\r\nicosahedral mature particle. Due to this, many fundamental questions on FV structural\r\nassembly mechanisms remain open. To answer these questions, was the main focus of this\r\nthesis.\r\nMainly, it is not known how FV assemble their core in a virus particle and what are the\r\nimportant assembly interaction sites within said core. What is the minimum assembly\r\ncompetent domain of FV Gag? Is there a morphological change in the assembly type of FVGag lattices? If so, what is defining these morphological shifts? Finally, it would be\r\ninteresting to know what is the evolutionary relationship between FV and the rest of the\r\nretrotranscribing elements, from a structural point of view?\r\nTo answer these questions, membrane-enveloped mammalian cell-derived FV virus-like\r\nparticles (VLPs) were produced. Cryo-electron tomography (cryo-ET) analysis suggested\r\nthese FV VLPs do not form a canonical retroviral Gag lattice structure, which is in line with\r\nearlier observations. To further evaluate FV Gag assembly competence and morphology,\r\nthe first bacterial cell-derived in vitro VLP assembly system was designed and optimized.\r\nUsing this system with different truncation variants, the minimum assembly competent\r\ndomain of FV Gag was found to be the putative CA300-477 domain. Varying VLP\r\nmorphologies were also observed and strongly suggested residues upstream of CA300-477\r\nplay a role in morphology determination. Finally, a combined cryo-electron microscopy (cryoEM) and cryo-ET approach was taken to analyze tubular assemblies from the minimal\r\nassembly competent domain. This revealed an unexpectedly unique non-canonical\r\nassembly architecture. Three novel lattice stabilizing interfaces were described which\r\nproved to be as unique as the lattice arrangement. Comparison to a newly published FV CA\r\ncore structure revealed the CA-CA interactions in the atypical assembly do not recapitulate\r\nwhat is described for the FV core lattice. However, the new in vitro VLP assembly system\r\nobtained in this thesis also provides an exciting opportunity to study still unresolved FV\r\nassembly features in a potentially facilitated approach compared to conventional methods.\r\nIn summary, this work provided a deeper understanding of the basic FV Gag assembly unit,\r\nas well as presenting the first FV Gag-derived in vitro VLP assembly system. This system\r\nreveals a novel and unique assembly architecture among retroviral in vitro assemblies." acknowledged_ssus: - _id: EM-Fac - _id: LifeSc - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Dario J full_name: Porley, Dario J id: 2FD6EA6C-F248-11E8-B48F-1D18A9856A87 last_name: Porley citation: ama: Porley Esteves D. Structural characterization of spumavirus capsid assemblies. 2024. doi:10.15479/at:ista:18101 apa: Porley Esteves, D. (2024). Structural characterization of spumavirus capsid assemblies. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18101 chicago: Porley Esteves, Darío. “Structural Characterization of Spumavirus Capsid Assemblies.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18101. ieee: D. Porley Esteves, “Structural characterization of spumavirus capsid assemblies,” Institute of Science and Technology Austria, 2024. ista: Porley Esteves D. 2024. Structural characterization of spumavirus capsid assemblies. Institute of Science and Technology Austria. mla: Porley Esteves, Darío. Structural Characterization of Spumavirus Capsid Assemblies. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18101. short: D. Porley Esteves, Structural Characterization of Spumavirus Capsid Assemblies, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-09-20T10:21:03Z date_published: 2024-09-26T00:00:00Z date_updated: 2026-04-07T13:21:01Z day: '26' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: FlSc doi: 10.15479/at:ista:18101 ec_funded: 1 file: - access_level: closed checksum: 3b8b0bacfe61112f3852744f3170e468 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: dporley date_created: 2024-09-26T13:40:33Z date_updated: 2025-03-25T23:30:03Z embargo_to: open_access file_id: '18149' file_name: PhD_thesis_DPorley_final_20240919.docx file_size: 14213128 relation: source_file - access_level: open_access checksum: 6c3a652a8eede874118e11d66a63652f content_type: application/pdf creator: dporley date_created: 2024-09-26T13:41:39Z date_updated: 2025-03-25T23:30:03Z embargo: 2025-03-25 file_id: '18150' file_name: PhD_thesis_DPorley_final_20240926_pdfa1.pdf file_size: 18583031 relation: main_file file_date_updated: 2025-03-25T23:30:03Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '131' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 9B9C98E0-BA93-11EA-9121-9846C619BF3A grant_number: '25762' name: Structural characterization of spumavirus capsid assemblies to understand conserved Ortervirales assembly mechanisms publication_identifier: isbn: - 978-3-99078-041-1 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Florian KM full_name: Schur, Florian KM id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 title: Structural characterization of spumavirus capsid assemblies type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_place: publisher _id: '17319' abstract: - lang: eng text: "This thesis comprises two distinct projects, each offering unique insights into fundamental\r\ncellular processes. While distinct in their focus, these different perspectives have a common\r\ntheme: chemiosmotic theory and utilisation of the proton gradient for driving the essential\r\nprocesses like auxin efflux and ATP synthesis, effectively bridging the membrane protein\r\nstructure and function from the realms of plant biology and cellular bioenergetics.\r\nThe first project of this thesis centres on the characterisation of PIN proteins, a class of\r\ntransmembrane transporters pivotal in the regulation of auxin transport and distribution in\r\nplants. PINs form a conserved and phylogenetically abundant group of transporters present in\r\nland plants and certain algae. Despite their great importance, they were one of the few elusive\r\nproteins essential for plant development not to be structurally and mechanistically\r\ncharacterised since their discovery almost 30 years ago. This work aimed to uncover the\r\nstructural and functional dynamics of the PIN protein-mediated auxin transport using an array\r\nof experimental techniques, including protein purification, biochemical assays and structural\r\nanalysis. Through an exhaustive screening process that took several years and included testing\r\ndifferent PIN homologues, expression systems, constructs, and purification conditions, we\r\ndeveloped a robust protocol for isolating the pure, stable, and monodisperse PIN8 protein.\r\nMoreover, utilising biophysical methods and buffer screening, we demonstrated that PIN8\r\nexhibits detergent and pH-dependent stability, with mild detergents and lower pH (5.0 and 6.0)\r\nbeing optimal for the stability of the protein. Using SEC-MALS and crosslinking, we\r\ndetermined that PIN8 forms dimers, which was confirmed by our structural studies. We\r\nobtained a cryo-EM map of PIN8 at pH 6.0, and, compared to recently published structures,\r\nour map implies major pH-dependent conformational changes and possibly utilisation of the\r\nproton gradient in the transport mechanism.\r\nThe subject of the second project was F1Fo-ATP synthase, an enzyme complex fundamental\r\nto cellular energy metabolism. Through an approach integrating biochemical assays and\r\nstructural analysis, this research aimed to unveil the molecular mechanism of inhibition of ATP\r\nsynthase by yaku´amide, a bioactive compound with potential therapeutic implications. Using\r\nsubmitochondrial particles and purified F1Fo-ATP synthase, we demonstrated that, contrary to\r\npublished data, yaku´amide inhibits both ATP hydrolysis and ATP synthesis reactions.\r\nMoreover, we found that yaku´amide inhibitory activity is proton motive force (pmf)\r\ndependent, with lower inhibition in a more coupled system. Utilising cryo-EM, we obtained\r\nmaps and models for the three main rotational states of murine ATP synthase (State 1 at 3.0 Å,\r\n8\r\nState 2 at 3.1 Å, and State 3 at 3.2 Å, overall). We observed several new features in our maps;\r\nhowever, we cannot definitively determine the exact mechanism of yaku amide’s inhibition on\r\nthe protein due to either resolution limits or suboptimal binding of the inhibitor." acknowledged_ssus: - _id: EM-Fac - _id: LifeSc alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Kristina full_name: Lukic, Kristina id: 2B04DB84-F248-11E8-B48F-1D18A9856A87 last_name: Lukic orcid: 0000-0003-1581-881X citation: ama: 'Lukic K. Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku’amide B. 2024. doi:10.15479/at:ista:17319' apa: 'Lukic, K. (2024). Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku’amide B. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17319' chicago: 'Lukic, Kristina. “Membrane Proteins in Plant Physiology and Bioenergetics : Investigating Auxin Efflux Transporter PIN8 and ATP Synthase Inhibition by the Novel Inhibitor Yaku’amide B.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17319.' ieee: 'K. Lukic, “Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku’amide B,” Institute of Science and Technology Austria, 2024.' ista: 'Lukic K. 2024. Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku’amide B. Institute of Science and Technology Austria.' mla: 'Lukic, Kristina. Membrane Proteins in Plant Physiology and Bioenergetics : Investigating Auxin Efflux Transporter PIN8 and ATP Synthase Inhibition by the Novel Inhibitor Yaku’amide B. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17319.' short: 'K. Lukic, Membrane Proteins in Plant Physiology and Bioenergetics : Investigating Auxin Efflux Transporter PIN8 and ATP Synthase Inhibition by the Novel Inhibitor Yaku’amide B, Institute of Science and Technology Austria, 2024.' corr_author: '1' date_created: 2024-07-26T09:05:55Z date_published: 2024-07-26T00:00:00Z date_updated: 2026-04-07T13:20:44Z day: '26' ddc: - '580' degree_awarded: PhD department: - _id: LeSa - _id: GradSch doi: 10.15479/at:ista:17319 file: - access_level: open_access checksum: 95517e697ea6a87e267e649cad560989 content_type: application/pdf creator: cchlebak date_created: 2024-07-26T13:14:24Z date_updated: 2025-01-26T23:30:04Z embargo: 2025-01-26 file_id: '17320' file_name: Thesis_Kristina_Lukic.pdf file_size: 24639084 relation: main_file - access_level: closed checksum: 74325746a9a05078fb9935dbf2aef752 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: cchlebak date_created: 2024-07-26T13:14:50Z date_updated: 2025-01-26T23:30:04Z embargo_to: open_access file_id: '17321' file_name: Thesis_Kristina_Lukic.docx file_size: 96334272 relation: source_file file_date_updated: 2025-01-26T23:30:04Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '224' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 title: 'Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku''amide B' type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_place: publisher _id: '17346' abstract: - lang: eng text: "Acquiring, retaining, and retrieving information over a wide range of timescales are crucial\r\nfunctions of the brain. The successful processing of memories affects many aspects of our\r\nlives and enables us and many other organisms to operate in a complex environment and\r\nto interact with it. In this context, the hippocampus and functionally connected brain\r\nareas, such as the prefrontal cortex, are central and have been subject to intensive research\r\nin the past decades. Storage of memories is believed to rely on distributed neural activity\r\nwithin these neural circuits. Additionally, neural memory traces of recent experience are\r\nreinstated during periods of rest or sleep. These reactivations are thought to play an\r\noutstanding role in the consolidation of memories and potentially facilitate the transfer of\r\ninformation from the hippocampus to cortical areas for long-term storage and integration\r\ninto existing knowledge.\r\nHowever, there is growing evidence that memory-related neural representations in the\r\nhippocampus are not as stable as initially thought and that they change even in the\r\nabsence of learning. It has been suggested that these changes reflect the accumulation of\r\nexperience, but the influence of interspersed consolidation periods has not been considered.\r\nPrevious studies have analyzed consolidation periods by detecting activity that strongly\r\nresembled neural activity during the acquisition of memory. Besides being often limited\r\nto only non-rapid eye movement (NREM) sleep, the used approaches were not capable of\r\ntracking changes in neural representations over extended temporal periods. More fluid\r\nrepresentations do not only challenge our understanding of how information is stored, but\r\nthey also affect the transfer of information between brain areas during the consolidation\r\nprocess.\r\nFor this thesis, I investigated the evolution of memory-related activity during sleep\r\nperiods expected to be involved in consolidation in the hippocampus and between the\r\nhippocampus and prefrontal cortex. I found that reactivated activity in the hippocampus\r\ngradually transformed during prolonged periods of sleep and inactivity. In the beginning,\r\nneural activity strongly resembled acquisition activity, whereas, with the progression of\r\ntime, it became more similar to the subsequent recall activity. NREM periods drove\r\nthis process, while rapid-eye movement (REM) periods showed a resetting effect. This\r\nreactivation drift was due to firing rate changes of a subset of cells and mirrored the\r\nrepresentational changes from the acquisition to the recall. A stable subset of cells\r\nwithstood the drift and maintained their activity. Therefore, my results indicate that\r\nmemory-related representations undergo spontaneous modifications during consolidation\r\nperiods and that these changes are predictive of representational drift.\r\nFurthermore, I found that the amount of change in the neural activity during subsequent\r\nsleep periods was biased by prior behavioral performance. Observed changes in the\r\nhippocampus and the prefrontal cortex were synchronized and increased after poor\r\nperformance, highlighting a potential role in the exchange of information. Low-variance\r\nvii\r\nperiods with distinct, more stable activity from a subset of cells significantly contributed\r\nto the heightened synchrony between both areas. Hence, interleaved phases of more stable\r\nneural activity could facilitate the information transfer between brain areas.\r\nIn conclusion, my investigations underline the fluidity of memory-related representations\r\nand assign a prominent role to sleep reactivation periods in their evolution. In addition, I\r\nidentified a potential mechanism of stable activity phases that might facilitate the synchronization across hippocampal-prefrontal activity despite ongoing changes. Reconciling\r\nand integrating findings from both spontaneous and behaviorally-related representational\r\nchanges in functionally related brain areas will help to broaden our understanding of how\r\nknowledge is stored, maintained, updated, and transferred between brain areas." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Lars full_name: Bollmann, Lars id: 47AD3038-F248-11E8-B48F-1D18A9856A87 last_name: Bollmann citation: ama: Bollmann L. Stability and change in the memory system during rest. 2024. doi:10.15479/at:ista:17346 apa: Bollmann, L. (2024). Stability and change in the memory system during rest. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17346 chicago: Bollmann, Lars. “Stability and Change in the Memory System during Rest.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17346. ieee: L. Bollmann, “Stability and change in the memory system during rest,” Institute of Science and Technology Austria, 2024. ista: Bollmann L. 2024. Stability and change in the memory system during rest. Institute of Science and Technology Austria. mla: Bollmann, Lars. Stability and Change in the Memory System during Rest. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17346. short: L. Bollmann, Stability and Change in the Memory System during Rest, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-07-29T15:08:42Z date_published: 2024-07-31T00:00:00Z date_updated: 2026-04-07T13:21:20Z day: '31' ddc: - '573' degree_awarded: PhD department: - _id: GradSch - _id: JoCs doi: 10.15479/at:ista:17346 file: - access_level: open_access checksum: 12c76297cc27449da80c60d79127770d content_type: application/pdf creator: lbollman date_created: 2024-07-31T18:37:19Z date_updated: 2025-01-31T23:30:03Z embargo: 2025-01-31 file_id: '17359' file_name: PhD_Thesis_Lars_Bollmann.pdf file_size: 12920169 relation: main_file - access_level: closed checksum: 19a0265079dec8038830ad6e35c5106e content_type: application/zip creator: lbollman date_created: 2024-07-31T18:38:39Z date_updated: 2025-01-31T23:30:03Z embargo_to: open_access file_id: '17360' file_name: Latex_source.zip file_size: 27568807 relation: source_file file_date_updated: 2025-01-31T23:30:03Z has_accepted_license: '1' keyword: - Memory - Hippocampus - Consolidation language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '103' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Jozsef L full_name: Csicsvari, Jozsef L id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 title: Stability and change in the memory system during rest type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_place: publisher _id: '17368' abstract: - lang: eng text: "Recent advancements in molecular diagnostic techniques have enabled the collection of\r\nmultiple types of omics data from patients, including genomics, epigenomics, proteomics,\r\nand transcriptomics. However, we lack effective methods for integrating all these different\r\ndata types and combining them with clinical outcomes to study the molecular mechanisms\r\nthat govern pathological phenotypes. We present multi-omics BayesW, a penalized Bayesian\r\nregression method that can handle general omics data for survival analysis of time-to-event\r\nphenotypes. Our method can: (1) accommodate incomplete data by allowing censored\r\nindividuals, (2) use continuous time-to-event data to test associations of markers with a\r\nphenotype and (3) estimate effects jointly while allowing for independent groups of biological\r\nmarkers. Extensive simulations using planted signals on real data demonstrate that our model\r\naccurately retrieves the true parameters of the model while controlling for false discoveries\r\nand maintaining the expected prediction accuracy. We address data correlations by estimating\r\nthe effects jointly, even between omic groups, while also estimating the individual variance\r\nexplained by each group. We apply our model to two datasets. Using 18,000 individuals from\r\nthe Generation Scotland study we model the association of time at onset of Type 2 Diabetes,\r\nStroke, Ischemic Disease, and Osteoarthritis from baseline study entry, with 831,724 CpG\r\nmethylation probes. We find that large proportions of variation in disease onset times can\r\nbe attributed to methylation as measured in whole blood at baseline in individuals without\r\ndisease symptoms. We then apply our model to The Cancer Genome Atlas (TCGA) pan-cancer\r\ndataset, in which we use 5 types of omics: copy number variation, epigenetics, somatic\r\nmutations, miRNA, and gene expression. For cancer survival age-at-onset we find that, when\r\nfitting the 5 groups together, almost all variation attributable to \"omics\" data is explained by\r\nDNA methylation. When considering progression times, both methylation and gene expression\r\nexplain a large part of the variance. We found 2 genes that are significantly associated (95%\r\nposterior inclusion probability) with cancer survival time, conditional on all other genome-wide\r\nomics data variation. Owing to the vast variability of mechanisms characterizing different\r\ncancers, there are likely few specific genes with a strong signal in a pan-cancer setting. Taken\r\ntogether, we showed the applicability of our multi-omics BayesW model to a wide-range of\r\nbiological questions in multi-omics data.\r\n" alternative_title: - ISTA Master's Thesis article_processing_charge: No author: - first_name: Ariadna full_name: Villanueva Marijuan, Ariadna id: e0ae4864-133f-11ed-8f02-adaa8dd27540 last_name: Villanueva Marijuan citation: ama: Villanueva Marijuan A. Bayesian linear regression for analyzing general omics data with time-to-event phenotypes. 2024. doi:10.15479/at:ista:17368 apa: Villanueva Marijuan, A. (2024). Bayesian linear regression for analyzing general omics data with time-to-event phenotypes. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17368 chicago: Villanueva Marijuan, Ariadna. “Bayesian Linear Regression for Analyzing General Omics Data with Time-to-Event Phenotypes.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17368. ieee: A. Villanueva Marijuan, “Bayesian linear regression for analyzing general omics data with time-to-event phenotypes,” Institute of Science and Technology Austria, 2024. ista: Villanueva Marijuan A. 2024. Bayesian linear regression for analyzing general omics data with time-to-event phenotypes. Institute of Science and Technology Austria. mla: Villanueva Marijuan, Ariadna. Bayesian Linear Regression for Analyzing General Omics Data with Time-to-Event Phenotypes. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17368. short: A. Villanueva Marijuan, Bayesian Linear Regression for Analyzing General Omics Data with Time-to-Event Phenotypes, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-08-02T10:52:40Z date_published: 2024-08-13T00:00:00Z date_updated: 2026-04-07T13:03:41Z day: '13' ddc: - '610' degree_awarded: MS department: - _id: GradSch - _id: MaRo doi: 10.15479/at:ista:17368 file: - access_level: open_access checksum: 0c2daa174609f0c00919dccc5701d375 content_type: application/pdf creator: avillanu date_created: 2024-08-14T11:51:24Z date_updated: 2025-02-14T23:30:03Z embargo: 2025-02-14 file_id: '17433' file_name: Masters_thesis_AriadnaVillanueva.pdf file_size: 13052436 relation: main_file - access_level: closed checksum: e9ed4465dfa539ac4c3a8d4d0b6271a1 content_type: application/zip creator: avillanu date_created: 2024-08-14T11:51:57Z date_updated: 2025-02-14T23:30:03Z embargo_to: open_access file_id: '17434' file_name: Masters thesis-AriadnaVillanueva.zip file_size: 45642547 relation: source_file file_date_updated: 2025-02-14T23:30:03Z has_accepted_license: '1' keyword: - Epigenetics - Multi-omics - Bayesian regression language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '60' publication_identifier: issn: - 2791-4585 publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 title: Bayesian linear regression for analyzing general omics data with time-to-event phenotypes tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_place: repository _id: '17465' abstract: - lang: eng text: "In the modern age of machine learning, artificial neural networks have become an integral part\r\nof many practical systems. One of the key ingredients of the success of the deep learning\r\napproach is recent computational advances which allowed the training of models with billions\r\nof parameters on large-scale data. Such over-parameterized and data-hungry regimes pose a\r\nchallenge for the theoretical analysis of modern models since “classical” statistical wisdom\r\nis no longer applicable. In this view, it is paramount to extend or develop new machinery\r\nthat will allow tackling the neural network analysis under new challenging asymptotic regimes,\r\nwhich is the focus of this thesis.\r\nLarge neural network systems are usually optimized via “local” search algorithms, such\r\nas stochastic gradient descent (SGD). However, given the high-dimensional nature of the\r\nparameter space, it is a priori not clear why such a crude “local” approach works so remarkably\r\nwell in practice. We take a step towards demystifying this phenomenon by showing that\r\nthe landscape of the SGD training dynamics exhibits a few beneficial properties for the\r\noptimization. First, we show that along the SGD trajectory an over-parameterized network\r\nis dropout stable. The emergence of dropout stability allows to conclude that the minima\r\nfound by SGD are connected via a continuous path of small loss. This in turn means that\r\nthe high-dimensional landscape of the neural network optimization problem is provably not so\r\nunfavourable to gradient-based training, due to mode connectivity. Next, we show that SGD\r\nfor an over-parameterized network tends to find solutions that are functionally more “simple”.\r\nThis in turn means that the SGD minima are more robust, since a less complicated solution\r\nwill less likely overfit the data. More formally, for a prototypical example of a wide two-layer\r\nReLU network on a 1d regression task we show that the SGD algorithm is implicitly selective in\r\nits choice of an interpolating solution. Namely, at convergence the neural network implements\r\na piece-wise linear function with the number of linear regions depending only on the amount\r\nof training data. This is in contrast to a “smooth”-like behaviour which one would expect\r\ngiven such a severe over-parameterization of the model.\r\nDiverging from the generic supervised setting of classification and regression problems, we\r\nanalyze an auto-encoder model that is commonly used for representation learning and data\r\ncompression. Despite the wide applicability of the auto-encoding paradigm, the theoretical\r\nunderstanding of their behaviour is limited even in the simplistic shallow case. The related\r\nwork is restricted to extreme asymptotic regimes in which the auto-encoder is either severely\r\nover-parameterized or under-parameterized. In contrast, we provide a tight characterization\r\nfor the 1-bit compression of Gaussian signals in the challenging proportional regime, i.e., the\r\ninput dimension and the size of the compressed representation obey the same asymptotics.\r\nWe also show that gradient-based methods are able to find a globally optimal solution and\r\nthat the predictions made for Gaussian data extrapolate beyond - to the case of compression\r\nof natural images. Next, we relax the Gaussian assumption and study more structured input\r\nsources. We show that the shallow model is sometimes agnostic to the structure of the data\r\nvii\r\nwhich results in a Gaussian-like behaviour. We prove that making the decoding component\r\nslightly less shallow is already enough to escape the “curse” of Gaussian performance.\r\n" acknowledged_ssus: - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Aleksandr full_name: Shevchenko, Aleksandr id: F2B06EC2-C99E-11E9-89F0-752EE6697425 last_name: Shevchenko citation: ama: Shevchenko A. High-dimensional limits in artificial neural networks. 2024. doi:10.15479/at:ista:17465 apa: Shevchenko, A. (2024). High-dimensional limits in artificial neural networks. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17465 chicago: Shevchenko, Alexander. “High-Dimensional Limits in Artificial Neural Networks.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17465. ieee: A. Shevchenko, “High-dimensional limits in artificial neural networks,” Institute of Science and Technology Austria, 2024. ista: Shevchenko A. 2024. High-dimensional limits in artificial neural networks. Institute of Science and Technology Austria. mla: Shevchenko, Alexander. High-Dimensional Limits in Artificial Neural Networks. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17465. short: A. Shevchenko, High-Dimensional Limits in Artificial Neural Networks, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-08-28T15:14:25Z date_published: 2024-08-29T00:00:00Z date_updated: 2026-06-18T17:55:53Z day: '29' ddc: - '519' degree_awarded: PhD department: - _id: GradSch - _id: DaAl - _id: MaMo doi: 10.15479/at:ista:17465 file: - access_level: open_access checksum: da6dd3166078934577f6af93d27000e2 content_type: application/pdf creator: ashevche date_created: 2024-09-02T09:23:32Z date_updated: 2024-10-05T22:30:05Z embargo: 2024-10-04 file_id: '17482' file_name: thesis_a2b.pdf file_size: 4468610 relation: main_file - access_level: closed checksum: 76a39ef252239560923cdda4ce0a31a4 content_type: application/zip creator: ashevche date_created: 2024-09-02T09:23:46Z date_updated: 2024-10-05T22:30:05Z embargo_to: open_access file_id: '17483' file_name: Thesis Alex - ISTA.zip file_size: 15930999 relation: source_file file_date_updated: 2024-10-05T22:30:05Z has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '232' project: - _id: 059876FA-7A3F-11EA-A408-12923DDC885E name: Prix Lopez-Loretta 2019 - Marco Mondelli - _id: 9B9290DE-BA93-11EA-9121-9846C619BF3A grant_number: W1260-N35 name: Vienna Graduate School on Computational Optimization publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '11420' relation: part_of_dissertation status: public - id: '14459' relation: part_of_dissertation status: public - id: '9198' relation: part_of_dissertation status: public - id: '17469' relation: part_of_dissertation status: public status: public supervisor: - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X title: High-dimensional limits in artificial neural networks type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2024' ... --- OA_place: publisher _id: '17881' abstract: - lang: eng text: "This work can be broadly classified into the study of critical phenomena in a one dimensional\r\narray of Josephson junctions. While we study quantum criticality when the array is in thermal\r\nequilibrium at zero bias, the non-equilibrium study involves understanding the bistability of the\r\narray at a critical non-zero bias. This work furthers our knowledge in understanding quantum\r\ncritical behaviour at finite temperatures in a one dimensional Josephson array, while also\r\nestablishing relaxation behaviour dual to that observed in a single Josephson junction.\r\nChapter 1 briefly introduces the model to understand superconductor-insulator phase transition\r\nin a one dimensional Josephson array and points out the state of the field from where we\r\nstarted our zero-bias experiments. In this context it discusses the phase-charge duality observed\r\nin a Josephson array and its dual hysteretic behaviour to that of a single junction, setting the\r\nground for our non-equilibrium study of the array.\r\nChapter 2 shows the experimental setup and the chip layout of the device we measured.\r\nIn chapter 3 we show that, unlike the typical quantum-critical broadening scenario, in one dimensional Josephson arrays temperature dramatically shifts the critical region. This shift leads\r\nto a regime of superconductivity at high temperature, arising from the melted zero-temperature\r\ninsulator. Our results quantitatively explain the low-temperature onset of superconductivity in\r\nnominally insulating regimes, and the transition to the strongly insulating phase. We further\r\npresent, to our knowledge, the first understanding of the onset of anomalous-metallic resistance\r\nsaturation [30]. This work demonstrates a non-trivial interplay between thermal effects and\r\nquantum criticality. A practical consequence is that, counterintuitively, the coherence of\r\nhigh-impedance quantum circuits is expected to be stabilized by thermal fluctuations.\r\nIn chapter 4, we show relaxation oscillations in a current-biased one dimensional array of\r\nJosephson junctions. These oscillations are well described by a circuit model, dual to the\r\nordinary Josephson relaxation oscillations [72]. Injection locking these oscillations results in\r\ncurrent plateaux. The relaxation step is found to obey a characteristic self-consistent relation,\r\nsuggesting that it is governed by overheating effects.\r\nChapter 5 describes the various checks and analysis we performed to support our conclusions\r\nmade in chapters 3 and 4.\r\nFinally, chapter 6 describes the nanofabrication steps and the finite element electromagnetic\r\nsimulations we performed to fabricate our devices." acknowledged_ssus: - _id: NanoFab - _id: M-Shop alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Soham full_name: Mukhopadhyay, Soham id: FDE60288-A89D-11E9-947F-1AF6E5697425 last_name: Mukhopadhyay orcid: 0000-0001-5263-5559 citation: ama: Mukhopadhyay S. Thermal effects in one dimensional Josephson chains. 2024. doi:10.15479/at:ista:17881 apa: Mukhopadhyay, S. (2024). Thermal effects in one dimensional Josephson chains. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17881 chicago: Mukhopadhyay, Soham. “Thermal Effects in One Dimensional Josephson Chains.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17881. ieee: S. Mukhopadhyay, “Thermal effects in one dimensional Josephson chains,” Institute of Science and Technology Austria, 2024. ista: Mukhopadhyay S. 2024. Thermal effects in one dimensional Josephson chains. Institute of Science and Technology Austria. mla: Mukhopadhyay, Soham. Thermal Effects in One Dimensional Josephson Chains. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17881. short: S. Mukhopadhyay, Thermal Effects in One Dimensional Josephson Chains, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-09-08T10:23:25Z date_published: 2024-09-10T00:00:00Z date_updated: 2026-06-03T07:16:04Z day: '10' ddc: - '539' degree_awarded: PhD department: - _id: GradSch - _id: AnHi doi: 10.15479/at:ista:17881 file: - access_level: open_access checksum: ed7763c3bbd59e1d7e1b664de3a26f3c content_type: application/pdf creator: smukhopa date_created: 2024-09-12T10:46:04Z date_updated: 2025-03-13T23:30:04Z embargo: 2025-03-13 file_id: '18059' file_name: PhD_Thesis_Soham_Mukhopadhyay.pdf file_size: 10297052 relation: main_file - access_level: closed checksum: e352667482701dd18a9a0e7418aef465 content_type: application/zip creator: smukhopa date_created: 2024-09-12T10:50:58Z date_updated: 2025-03-13T23:30:04Z embargo_to: open_access file_id: '18060' file_name: PhD_Thesis_Soham_Mukhopadhyay_source.zip file_size: 29178634 relation: source_file file_date_updated: 2025-03-13T23:30:04Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '82' project: - _id: 0aa3608a-070f-11eb-9043-e9cd8a2bd931 grant_number: P33692 name: Cavity electromechanics across a quantum phase transition publication_identifier: isbn: - 978-3-99078-043-5 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '14032' relation: part_of_dissertation status: public - id: '18057' relation: part_of_dissertation status: public status: public supervisor: - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 title: Thermal effects in one dimensional Josephson chains type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- _id: '17469' abstract: - lang: eng text: 'Autoencoders are a prominent model in many empirical branches of machine learning and lossy data compression. However, basic theoretical questions remain unanswered even in a shallow two-layer setting. In particular, to what degree does a shallow autoencoder capture the structure of the underlying data distribution? For the prototypical case of the 1-bit compression of sparse Gaussian data, we prove that gradient descent converges to a solution that completely disregards the sparse structure of the input. Namely, the performance of the algorithm is the same as if it was compressing a Gaussian source - with no sparsity. For general data distributions, we give evidence of a phase transition phenomenon in the shape of the gradient descent minimizer, as a function of the data sparsity: below the critical sparsity level, the minimizer is a rotation taken uniformly at random (just like in the compression of non-sparse data); above the critical sparsity, the minimizer is the identity (up to a permutation). Finally, by exploiting a connection with approximate message passing algorithms, we show how to improve upon Gaussian performance for the compression of sparse data: adding a denoising function to a shallow architecture already reduces the loss provably, and a suitable multi-layer decoder leads to a further improvement. We validate our findings on image datasets, such as CIFAR-10 and MNIST.' acknowledgement: "Kevin Kogler, Alexander Shevchenko and Marco Mondelli are supported by the 2019 Lopez-Loreta Prize. Hamed\r\nHassani acknowledges the support by the NSF CIF award (1910056) and the NSF Institute for CORE Emerging Methods in Data Science (EnCORE)." alternative_title: - PMLR article_processing_charge: No arxiv: 1 author: - first_name: Kevin full_name: Kögler, Kevin id: 94ec913c-dc85-11ea-9058-e5051ab2428b last_name: Kögler - first_name: Aleksandr full_name: Shevchenko, Aleksandr id: F2B06EC2-C99E-11E9-89F0-752EE6697425 last_name: Shevchenko - first_name: Hamed full_name: Hassani, Hamed last_name: Hassani - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 citation: ama: 'Kögler K, Shevchenko A, Hassani H, Mondelli M. Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth. In: Proceedings of the 41st International Conference on Machine Learning. Vol 235. ML Research Press; 2024:24964-25015.' apa: 'Kögler, K., Shevchenko, A., Hassani, H., & Mondelli, M. (2024). Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth. In Proceedings of the 41st International Conference on Machine Learning (Vol. 235, pp. 24964–25015). Vienna, Austria: ML Research Press.' chicago: 'Kögler, Kevin, Alexander Shevchenko, Hamed Hassani, and Marco Mondelli. “Compression of Structured Data with Autoencoders: Provable Benefit of Nonlinearities and Depth.” In Proceedings of the 41st International Conference on Machine Learning, 235:24964–15. ML Research Press, 2024.' ieee: 'K. Kögler, A. Shevchenko, H. Hassani, and M. Mondelli, “Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth,” in Proceedings of the 41st International Conference on Machine Learning, Vienna, Austria, 2024, vol. 235, pp. 24964–25015.' ista: 'Kögler K, Shevchenko A, Hassani H, Mondelli M. 2024. Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth. Proceedings of the 41st International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 235, 24964–25015.' mla: 'Kögler, Kevin, et al. “Compression of Structured Data with Autoencoders: Provable Benefit of Nonlinearities and Depth.” Proceedings of the 41st International Conference on Machine Learning, vol. 235, ML Research Press, 2024, pp. 24964–5015.' short: K. Kögler, A. Shevchenko, H. Hassani, M. Mondelli, in:, Proceedings of the 41st International Conference on Machine Learning, ML Research Press, 2024, pp. 24964–25015. conference: end_date: 2024-07-27 location: Vienna, Austria name: 'ICML: International Conference on Machine Learning' start_date: 2024-07-21 corr_author: '1' date_created: 2024-08-29T11:47:57Z date_published: 2024-07-01T00:00:00Z date_updated: 2026-07-16T22:30:49Z day: '01' ddc: - '000' department: - _id: DaAl - _id: MaMo external_id: arxiv: - '2402.05013' intvolume: ' 235' language: - iso: eng main_file_link: - open_access: '1' url: https://proceedings.mlr.press/v235/kogler24a.html month: '07' oa: 1 oa_version: Published Version page: 24964-25015 project: - _id: 059876FA-7A3F-11EA-A408-12923DDC885E name: Prix Lopez-Loretta 2019 - Marco Mondelli publication: Proceedings of the 41st International Conference on Machine Learning publication_status: published publisher: ML Research Press quality_controlled: '1' related_material: record: - id: '17465' relation: dissertation_contains status: public scopus_import: '1' status: public title: 'Compression of structured data with autoencoders: Provable benefit of nonlinearities and depth' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 235 year: '2024' ...